commit dataset card

README.md

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+---
+task_categories:
+  - keypoint-detection
+license: cc-by-4.0
+tags:
+  - biology
+  - pose-estimation
+  - multiview
+  - fly
+  - lightning-pose
+pretty_name: Fly Anipose (Lightning Pose subset)
+size_categories:
+  - 1K<n<10K
+---
+
+# Fly Anipose — Lightning Pose Multiview Dataset
+
+6-camera pose estimation dataset for *Drosophila* leg keypoints, packaged for use with [Lightning Pose](https://github.com/danbider/lightning-pose).
+
+## Dataset Description
+
+Head-fixed flies run on a spherical treadmill while 6 synchronized cameras capture locomotion at **300 Hz**. Each frame is labeled with **30 keypoints** — 5 joint segments (A–E) on each of 6 legs (left legs L1–L3, right legs R1–R3).
+
+Labels are **filtered Anipose predictions**, not hand-labeled frames. They were constructed by:
+1. Removing instances with mean 3D reprojection error > 10 px
+2. Running k-means on 3D poses and keeping 25 instances per session
+3. Using filtered 2D predictions; setting keypoints with 2D reprojection error > 10 px to NaN
+
+Source data: Karashchuk et al., *Cell Reports* 2021 — original archive at https://doi.org/10.5061/dryad.nzs7h44s4
+
+## Data Splits
+
+| Split | Labeled instances | Sessions |
+|-------|----------------:|--------:|
+| In-distribution (InD) | 377 | 16 |
+| Out-of-distribution (OOD) | 300 | 12 |
+
+InD and OOD sets contain **different animals/sessions** (no overlap).
+
+- `CollectedData_Cam-{A-F}.csv` — InD labels; `videos/` — InD videos
+- `CollectedData_Cam-{A-F}_new.csv` — OOD labels; `videos_new/` — OOD videos
+
+## Keypoints
+
+30 keypoints total: side (`L`/`R`) + leg number (`1`–`3`) + segment (`A`–`E`, proximal→distal).
+
+| Left legs | Right legs |
+|-----------|------------|
+| L1A, L1B, L1C, L1D, L1E | R1A, R1B, R1C, R1D, R1E |
+| L2A, L2B, L2C, L2D, L2E | R2A, R2B, R2C, R2D, R2E |
+| L3A, L3B, L3C, L3D, L3E | R3A, R3B, R3C, R3D, R3E |
+
+## Directory Structure
+
+```
+fly_anipose_subset/
+├── labeled-data/           # Extracted frames per session×view; includes ±2 context frames
+├── videos/                 # Full InD session videos (<SessionKey>_<View>.mp4)
+├── calibrations/           # Per-session camera calibration (.toml) for 3D features
+├── calibrations.csv        # InD calibration index
+├── calibrations_new.csv    # OOD calibration index
+├── CollectedData_Cam-{A-F}.csv      # InD 2D keypoint labels (x,y per keypoint)
+├── CollectedData_Cam-{A-F}_new.csv  # OOD 2D keypoint labels
+├── config_fly-anipose.yaml # Sample Lightning Pose training config
+├── project.yaml            # View and keypoint definitions (required by LP App)
+└── models/                 # Pre-trained model checkpoints
+    ├── baseline/
+    ├── seed1/
+    ├── seed2/
+    └── pleasant_ensemble/
+```
+
+See the Lightning Pose documentation for full details on the [multiview data directory structure](https://lightning-pose.readthedocs.io/en/latest/source/directory_structure_reference/multiview_structure.html) and [model directory structure](https://lightning-pose.readthedocs.io/en/latest/source/directory_structure_reference/model_dir_structure.html).
+
+## Usage with Lightning Pose
+
+The included `config_fly-anipose.yaml` is a ready-to-use training config. Key settings:
+
+- **Image resize:** 256 × 256
+- **Backbone:** `resnet50_animal_ap10k`
+- **Views:** Cam-A through Cam-F
+- **Keypoints:** 30
+
+Update `data.data_dir` and `data.video_dir` to absolute paths on your machine before training.
+
+```bash
+python scripts/train_hydra.py --config-path /path/to/fly_anipose_subset \
+    --config-name config_fly-anipose
+```
+
+## Citation
+
+If you use this dataset, please cite the original Anipose paper:
+
+```bibtex
+@article{karashchuk2021anipose,
+  title   = {Anipose: A toolkit for robust markerless 3D pose estimation},
+  author  = {Karashchuk, Pierre and Rupp, Katie L and Dickinson, Evyn S and
+             Walling-Bell, Sarah and Sanders, Elisha and Azim, Eiman and
+             Brunton, Bingni W and Tuthill, John C},
+  journal = {Cell Reports},
+  volume  = {36},
+  number  = {13},
+  year    = {2021},
+  doi     = {10.1016/j.celrep.2021.109730}
+}
+```
+
+Original data archive: https://doi.org/10.5061/dryad.nzs7h44s4